CleanSweep and other installation monitors can monitor all disk activity during a program's installation. If you are installing some application, say ProgramX, and CleanSweep is monitoring the installation it assumes that all disk activity is related to the ProgramX's installation. If Second Copy is running in the background at the same time and copying files, CleanSweep wrongly assumes that the files copied by Second Copy and updates to the Second Copy profile are also related to ProgramX's installation. Later, if you use ClearnSweep's automatic uninstallation routine to remove ProgramX, it may delete Second Copy profiles and other files.
Do not use CleanSweep's automatic uninstall feature (use the manual feature and make sure to skip over any unrelated entries) or exit all other background applications, such as Second Copy, before monitoring ProgramX's installation.